kkonganti@11: process BWA_IDX_MEM {
kkonganti@11:     tag "$meta.id"
kkonganti@11:     label 'process_micro'
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${params.swmodulepath}${params.fs}bwa${params.fs}0.7.17" : null)
kkonganti@11:     conda (params.enable_conda ? "bioconda::bwa=0.7.17 conda-forge::perl" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://depot.galaxyproject.org/singularity/bwa:0.7.17--he4a0461_11' :
kkonganti@11:         'quay.io/biocontainers/bwa:0.7.17--he4a0461_11' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         tuple val(meta), path(genome), path(reads)
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         tuple val(meta), path("*.sam"), emit: aligned_sam
kkonganti@11:         path  "versions.yml"          , emit: versions
kkonganti@11: 
kkonganti@11:     when:
kkonganti@11:         
kkonganti@11: 
kkonganti@11:     script:
kkonganti@11:         def args   = task.ext.args ?: ''
kkonganti@11:         def args2  = task.ext.args2 ?: ''
kkonganti@11:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@11:         """
kkonganti@11: 
kkonganti@11:         bwa index $args $genome
kkonganti@11:         if [ "${params.fq_single_end}" = "false" ]; then
kkonganti@11:             bwa mem \\
kkonganti@11:                 $args2 \\
kkonganti@11:                 -t $task.cpus \\
kkonganti@11:                 -a $genome \\
kkonganti@11:                 ${reads[0]} > ${prefix}.aligned_1.sam
kkonganti@11:             bwa mem \\
kkonganti@11:                 $args2 \\
kkonganti@11:                 -t $task.cpus \\
kkonganti@11:                 -a $genome \\
kkonganti@11:                 ${reads[1]} > ${prefix}.aligned_2.sam
kkonganti@11:         else
kkonganti@11:             bwa mem \\
kkonganti@11:                 $args2 \\
kkonganti@11:                 -t $task.cpus \\
kkonganti@11:                 -a $genome \\
kkonganti@11:                 $reads > ${prefix}.aligned.sam 
kkonganti@11: 
kkonganti@11:         fi
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
kkonganti@11:         END_VERSIONS
kkonganti@11:         """
kkonganti@11: }